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    <div id="content"><h1>Class: Ensembl::Variation::TranscriptVariation
  
  
  
</h1>

<dl class="box">
  
    <dt class="r1">Inherits:</dt>
    <dd class="r1">
      <span class="inheritName"><span class='object_link'><a href="DBConnection.html" title="Ensembl::Variation::DBConnection (class)">DBConnection</a></span></span>
      
        <ul class="fullTree">
          <li>Object</li>
          
            <li class="next">ActiveRecord::Base</li>
          
            <li class="next"><span class='object_link'><a href="../DBRegistry/Base.html" title="Ensembl::DBRegistry::Base (class)">DBRegistry::Base</a></span></li>
          
            <li class="next"><span class='object_link'><a href="DBConnection.html" title="Ensembl::Variation::DBConnection (class)">DBConnection</a></span></li>
          
            <li class="next">Ensembl::Variation::TranscriptVariation</li>
          
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      </dd>
    
  
  
    
  
    
  
  
  
    <dt class="r2 last">Defined in:</dt>
    <dd class="r2 last">lib/ensembl/variation/variation.rb</dd>
  
</dl>
<div class="clear"></div>

<h2>Overview</h2><div class="docstring">
  <div class="discussion">
    <p>
The TranscriptVariation class gives information about the position of a
VariationFeature, mapped on an annotated transcript.
</p>
<p>
This class uses ActiveRecord to access data in the Ensembl database. See
the general documentation of the Ensembl module for more information on
what this means and what methods are available.
</p>


  </div>
</div>
<div class="tags">
  
  <div class="examples">
    <h3>Examples:</h3>
    
      <h4><div class='inline'></div></h4>
      <pre class="example code"><span class='vf identifier id'>vf</span> <span class='assign token'>=</span> <span class='Variation constant id'>Variation</span><span class='dot token'>.</span><span class='find_by_name identifier id'>find_by_name</span><span class='lparen token'>(</span><span class='string val'>'rs10111'</span><span class='rparen token'>)</span><span class='dot token'>.</span><span class='variation_feature identifier id'>variation_feature</span>
<span class='vf identifier id'>vf</span><span class='dot token'>.</span><span class='transcript_variations identifier id'>transcript_variations</span><span class='dot token'>.</span><span class='each identifier id'>each</span> <span class='do do kw'>do</span> <span class='bitor op'>|</span><span class='tv identifier id'>tv</span><span class='bitor op'>|</span>
  <span class='puts identifier id'>puts</span> <span class='tv identifier id'>tv</span><span class='dot token'>.</span><span class='peptide_allele_string identifier id'>peptide_allele_string</span><span class='comma token'>,</span> <span class='tv identifier id'>tv</span><span class='dot token'>.</span><span class='transcript identifier id'>transcript</span><span class='dot token'>.</span><span class='stable_id identifier id'>stable_id</span>    
<span class='end end kw'>end</span>
</pre>
    
  </div>

</div>

  
  
  
  
  
  
  
  
  

  
    <h2>
      Instance Method Summary
      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
    </h2>

    <ul class="summary">
      
        <li class="public ">
  <span class="summary_signature">
    
      <a href="#consequence_type-instance_method" title="#consequence_type (instance method)">- (Object) <strong>consequence_type</strong> </a>
    

    
  </span>
  
  
  
  
  
  

  
    <span class="summary_desc"><div class='inline'><p>
workaround as ActiveRecord do not parse SET field in MySQL.
</p>
</div></span>
  
</li>

      
        <li class="public ">
  <span class="summary_signature">
    
      <a href="#transcript-instance_method" title="#transcript (instance method)">- (Object) <strong>transcript</strong> </a>
    

    
  </span>
  
  
  
  
  
  

  
    <span class="summary_desc"><div class='inline'></div></span>
  
</li>

      
    </ul>
  


  
  
  
  
  
  
  
  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="DBConnection.html" title="Ensembl::Variation::DBConnection (class)">DBConnection</a></span></h3>
  <p class="inherited"><span class='object_link'><a href="DBConnection.html#connect-class_method" title="Ensembl::Variation::DBConnection.connect (method)">connect</a></span>, <span class='object_link'><a href="DBConnection.html#ensemblgenomes_connect-class_method" title="Ensembl::Variation::DBConnection.ensemblgenomes_connect (method)">ensemblgenomes_connect</a></span></p>

  
  
  
  
  
  
  
  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="../DBRegistry/Base.html" title="Ensembl::DBRegistry::Base (class)">DBRegistry::Base</a></span></h3>
  <p class="inherited"><span class='object_link'><a href="../DBRegistry/Base.html#generic_connect-class_method" title="Ensembl::DBRegistry::Base.generic_connect (method)">generic_connect</a></span>, <span class='object_link'><a href="../DBRegistry/Base.html#get_info-class_method" title="Ensembl::DBRegistry::Base.get_info (method)">get_info</a></span>, <span class='object_link'><a href="../DBRegistry/Base.html#get_name_from_db-class_method" title="Ensembl::DBRegistry::Base.get_name_from_db (method)">get_name_from_db</a></span></p>

  

  <div id="instance_method_details" class="method_details_list">
    <h2>Instance Method Details</h2>
    
    
      <div class="method_details first">
  <p class="signature first" id="consequence_type-instance_method">
  
    - (<tt>Object</tt>) <strong>consequence_type</strong> 
  

  
</p><div class="docstring">
  <div class="discussion">
    <p>
workaround as ActiveRecord do not parse SET field in MySQL
</p>


  </div>
</div>
<div class="tags">
  
</div><table class="source_code">
  <tr>
    <td>
      <pre class="lines">


379
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381</pre>
    </td>
    <td>
      <pre class="code"><span class="info file"># File 'lib/ensembl/variation/variation.rb', line 379</span>

<span class='def def kw'>def</span> <span class='consequence_type identifier id'>consequence_type</span> 
  <span class='dstring node'>&quot;#{attributes_before_type_cast['consequence_type']}&quot;</span> 
<span class='end end kw'>end</span>
</pre>
    </td>
  </tr>
</table>
</div>
    
      <div class="method_details ">
  <p class="signature " id="transcript-instance_method">
  
    - (<tt>Object</tt>) <strong>transcript</strong> 
  

  
</p><table class="source_code">
  <tr>
    <td>
      <pre class="lines">


383
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    </td>
    <td>
      <pre class="code"><span class="info file"># File 'lib/ensembl/variation/variation.rb', line 383</span>

<span class='def def kw'>def</span> <span class='transcript identifier id'>transcript</span>
  <span class='host identifier id'>host</span><span class='comma token'>,</span><span class='user identifier id'>user</span><span class='comma token'>,</span><span class='password identifier id'>password</span><span class='comma token'>,</span><span class='db_name identifier id'>db_name</span><span class='comma token'>,</span><span class='port identifier id'>port</span><span class='comma token'>,</span><span class='species identifier id'>species</span><span class='comma token'>,</span><span class='release identifier id'>release</span> <span class='assign token'>=</span> <span class='Ensembl constant id'>Ensembl</span><span class='colon2 op'>::</span><span class='Variation constant id'>Variation</span><span class='colon2 op'>::</span><span class='DBConnection constant id'>DBConnection</span><span class='dot token'>.</span><span class='get_info identifier id'>get_info</span>
  <span class='if if kw'>if</span> <span class='notop op'>!</span><span class='Ensembl constant id'>Ensembl</span><span class='colon2 op'>::</span><span class='Core constant id'>Core</span><span class='colon2 op'>::</span><span class='DBConnection constant id'>DBConnection</span><span class='dot token'>.</span><span class='connected? fid id'>connected?</span> <span class='then then kw'>then</span>     
      <span class='Ensembl constant id'>Ensembl</span><span class='colon2 op'>::</span><span class='Core constant id'>Core</span><span class='colon2 op'>::</span><span class='DBConnection constant id'>DBConnection</span><span class='dot token'>.</span><span class='connect identifier id'>connect</span><span class='lparen token'>(</span><span class='species identifier id'>species</span><span class='comma token'>,</span><span class='release identifier id'>release</span><span class='dot token'>.</span><span class='to_i identifier id'>to_i</span><span class='comma token'>,</span><span class='symbol val'>:username</span> <span class='assign token'>=</span><span class='gt op'>&gt;</span> <span class='user identifier id'>user</span><span class='comma token'>,</span> <span class='symbol val'>:password</span> <span class='assign token'>=</span><span class='gt op'>&gt;</span> <span class='password identifier id'>password</span><span class='comma token'>,</span><span class='symbol val'>:host</span> <span class='assign token'>=</span><span class='gt op'>&gt;</span> <span class='host identifier id'>host</span><span class='comma token'>,</span> <span class='symbol val'>:port</span> <span class='assign token'>=</span><span class='gt op'>&gt;</span> <span class='port identifier id'>port</span><span class='rparen token'>)</span>    
  <span class='end end kw'>end</span>
  
  <span class='begin begin kw'>begin</span> <span class='comment val'># this changed from release 58</span>
    <span class='return return kw'>return</span> <span class='Ensembl constant id'>Ensembl</span><span class='colon2 op'>::</span><span class='Core constant id'>Core</span><span class='colon2 op'>::</span><span class='Transcript constant id'>Transcript</span><span class='dot token'>.</span><span class='find_by_stable_id identifier id'>find_by_stable_id</span><span class='lparen token'>(</span><span class='self self kw'>self</span><span class='dot token'>.</span><span class='transcript_stable_id identifier id'>transcript_stable_id</span><span class='rparen token'>)</span>
  <span class='rescue rescue kw'>rescue</span> <span class='NoMethodError constant id'>NoMethodError</span>  
    <span class='return return kw'>return</span> <span class='Ensembl constant id'>Ensembl</span><span class='colon2 op'>::</span><span class='Core constant id'>Core</span><span class='colon2 op'>::</span><span class='Transcript constant id'>Transcript</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='self self kw'>self</span><span class='dot token'>.</span><span class='transcript_id identifier id'>transcript_id</span><span class='rparen token'>)</span>
  <span class='end end kw'>end</span>
  
<span class='end end kw'>end</span>
</pre>
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